Starting phenix.real_space_refine on Sat Aug 3 17:24:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzp_27804/08_2024/8dzp_27804.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzp_27804/08_2024/8dzp_27804.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzp_27804/08_2024/8dzp_27804.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzp_27804/08_2024/8dzp_27804.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzp_27804/08_2024/8dzp_27804.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dzp_27804/08_2024/8dzp_27804.cif" } resolution = 2.71 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 62 5.16 5 C 5524 2.51 5 N 1443 2.21 5 O 1628 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 155": "OD1" <-> "OD2" Residue "B GLU 8": "OE1" <-> "OE2" Residue "B ASP 9": "OD1" <-> "OD2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 231": "OD1" <-> "OD2" Residue "B ASP 251": "OD1" <-> "OD2" Residue "B ASP 341": "OD1" <-> "OD2" Residue "C ASP 153": "OD1" <-> "OD2" Residue "C PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 195": "OD1" <-> "OD2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E GLU 222": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 8657 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2160 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 9, 'TRANS': 270} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 84 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 4, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1691 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 211} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2593 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 399 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'U99': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.33, per 1000 atoms: 0.62 Number of scatterers: 8657 At special positions: 0 Unit cell: (90.64, 123.2, 125.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 62 16.00 O 1628 8.00 N 1443 7.00 C 5524 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 210 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.35 Conformation dependent library (CDL) restraints added in 1.4 seconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2104 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 14 sheets defined 36.7% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 58 through 63 removed outlier: 4.008A pdb=" N ILE A 61 " --> pdb=" O ILE A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 86 removed outlier: 4.204A pdb=" N PHE A 70 " --> pdb=" O TYR A 66 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLY A 73 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU A 79 " --> pdb=" O VAL A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 111 removed outlier: 3.516A pdb=" N ILE A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR A 111 " --> pdb=" O LEU A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 121 removed outlier: 3.771A pdb=" N GLN A 115 " --> pdb=" O THR A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 162 Processing helix chain 'A' and resid 165 through 170 Processing helix chain 'A' and resid 171 through 196 removed outlier: 3.588A pdb=" N SER A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 235 Processing helix chain 'A' and resid 235 through 254 Processing helix chain 'A' and resid 263 through 300 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 305 through 326 removed outlier: 3.506A pdb=" N LEU A 309 " --> pdb=" O SER A 305 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER A 323 " --> pdb=" O GLY A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.796A pdb=" N ARG A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.800A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.605A pdb=" N LYS B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 270 through 278 Processing helix chain 'B' and resid 282 through 286 removed outlier: 4.067A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 329 through 351 removed outlier: 3.838A pdb=" N VAL B 335 " --> pdb=" O ASN B 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.788A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.717A pdb=" N VAL E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 201 Processing sheet with id=AA2, first strand: chain 'B' and resid 185 through 191 removed outlier: 8.515A pdb=" N ALA B 220 " --> pdb=" O GLU B 33 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N ALA B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 51 removed outlier: 6.763A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 6.908A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.189A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.987A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.545A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.902A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.498A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.596A pdb=" N SER C 245 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N THR C 249 " --> pdb=" O SER C 245 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.721A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.170A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.170A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB5, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.536A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1251 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1581 1.33 - 1.45: 2279 1.45 - 1.57: 4883 1.57 - 1.69: 0 1.69 - 1.81: 90 Bond restraints: 8833 Sorted by residual: bond pdb=" N ASP B 200 " pdb=" CA ASP B 200 " ideal model delta sigma weight residual 1.456 1.481 -0.025 1.21e-02 6.83e+03 4.16e+00 bond pdb=" N TYR E 223 " pdb=" CA TYR E 223 " ideal model delta sigma weight residual 1.456 1.478 -0.023 1.13e-02 7.83e+03 4.03e+00 bond pdb=" CA THR B 48 " pdb=" C THR B 48 " ideal model delta sigma weight residual 1.522 1.548 -0.026 1.33e-02 5.65e+03 3.89e+00 bond pdb=" N PRO E 224 " pdb=" CA PRO E 224 " ideal model delta sigma weight residual 1.469 1.444 0.025 1.28e-02 6.10e+03 3.80e+00 bond pdb=" C PRO E 224 " pdb=" O PRO E 224 " ideal model delta sigma weight residual 1.235 1.211 0.024 1.30e-02 5.92e+03 3.34e+00 ... (remaining 8828 not shown) Histogram of bond angle deviations from ideal: 97.07 - 104.46: 106 104.46 - 111.85: 4268 111.85 - 119.24: 3016 119.24 - 126.64: 4480 126.64 - 134.03: 123 Bond angle restraints: 11993 Sorted by residual: angle pdb=" C TYR E 223 " pdb=" CA TYR E 223 " pdb=" CB TYR E 223 " ideal model delta sigma weight residual 110.44 105.08 5.36 9.00e-01 1.23e+00 3.55e+01 angle pdb=" N PRO E 224 " pdb=" CA PRO E 224 " pdb=" CB PRO E 224 " ideal model delta sigma weight residual 103.25 99.25 4.00 1.05e+00 9.07e-01 1.45e+01 angle pdb=" N ASP B 200 " pdb=" CA ASP B 200 " pdb=" CB ASP B 200 " ideal model delta sigma weight residual 110.57 116.19 -5.62 1.57e+00 4.06e-01 1.28e+01 angle pdb=" C ALA A 57 " pdb=" N ILE A 58 " pdb=" CA ILE A 58 " ideal model delta sigma weight residual 122.13 128.54 -6.41 1.85e+00 2.92e-01 1.20e+01 angle pdb=" CA ILE A 58 " pdb=" CB ILE A 58 " pdb=" CG2 ILE A 58 " ideal model delta sigma weight residual 110.50 115.95 -5.45 1.70e+00 3.46e-01 1.03e+01 ... (remaining 11988 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.08: 5006 24.08 - 48.16: 239 48.16 - 72.24: 25 72.24 - 96.32: 4 96.32 - 120.40: 1 Dihedral angle restraints: 5275 sinusoidal: 2021 harmonic: 3254 Sorted by residual: dihedral pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " pdb=" CA PRO E 224 " ideal model delta harmonic sigma weight residual 180.00 59.60 120.40 0 5.00e+00 4.00e-02 5.80e+02 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 167.02 -74.02 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CA ALA E 229 " pdb=" C ALA E 229 " pdb=" N GLY E 230 " pdb=" CA GLY E 230 " ideal model delta harmonic sigma weight residual -180.00 -161.14 -18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1207 0.068 - 0.135: 176 0.135 - 0.203: 11 0.203 - 0.270: 3 0.270 - 0.338: 2 Chirality restraints: 1399 Sorted by residual: chirality pdb=" C22 U99 A 401 " pdb=" C20 U99 A 401 " pdb=" C23 U99 A 401 " pdb=" C8 U99 A 401 " both_signs ideal model delta sigma weight residual False -2.23 -1.89 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CB ILE A 58 " pdb=" CA ILE A 58 " pdb=" CG1 ILE A 58 " pdb=" CG2 ILE A 58 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CG LEU E 162 " pdb=" CB LEU E 162 " pdb=" CD1 LEU E 162 " pdb=" CD2 LEU E 162 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1396 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 222 " -0.017 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C GLU E 222 " 0.061 2.00e-02 2.50e+03 pdb=" O GLU E 222 " -0.023 2.00e-02 2.50e+03 pdb=" N TYR E 223 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.044 5.00e-02 4.00e+02 6.59e-02 6.95e+00 pdb=" N PRO C 236 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 337 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C ASP B 337 " 0.042 2.00e-02 2.50e+03 pdb=" O ASP B 337 " -0.016 2.00e-02 2.50e+03 pdb=" N ALA B 338 " -0.014 2.00e-02 2.50e+03 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 973 2.75 - 3.29: 8030 3.29 - 3.83: 14569 3.83 - 4.36: 17170 4.36 - 4.90: 30204 Nonbonded interactions: 70946 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.216 3.040 nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP C 163 " pdb=" OG1 THR C 165 " model vdw 2.283 3.040 nonbonded pdb=" OG SER B 6 " pdb=" OD1 ASP B 9 " model vdw 2.302 3.040 nonbonded pdb=" O THR A 150 " pdb=" OG SER A 153 " model vdw 2.334 3.040 ... (remaining 70941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.310 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8833 Z= 0.229 Angle : 0.675 8.930 11993 Z= 0.372 Chirality : 0.048 0.338 1399 Planarity : 0.006 0.066 1503 Dihedral : 13.618 120.400 3165 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.11 % Allowed : 0.75 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.24), residues: 1100 helix: 0.49 (0.25), residues: 371 sheet: 0.30 (0.29), residues: 285 loop : -1.35 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 82 HIS 0.011 0.001 HIS C 62 PHE 0.015 0.002 PHE A 143 TYR 0.021 0.002 TYR E 178 ARG 0.013 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 192 time to evaluate : 0.896 Fit side-chains REVERT: B 225 VAL cc_start: 0.8319 (t) cc_final: 0.8118 (t) REVERT: B 269 ASN cc_start: 0.8395 (m110) cc_final: 0.8058 (m110) REVERT: B 275 GLU cc_start: 0.7065 (tt0) cc_final: 0.6770 (tt0) REVERT: B 337 ASP cc_start: 0.7171 (m-30) cc_final: 0.6868 (m-30) REVERT: C 219 ARG cc_start: 0.7254 (mmt90) cc_final: 0.6935 (mmt90) REVERT: C 258 ASP cc_start: 0.6739 (t70) cc_final: 0.6498 (t70) REVERT: E 89 GLU cc_start: 0.7146 (mp0) cc_final: 0.6855 (mp0) outliers start: 1 outliers final: 2 residues processed: 192 average time/residue: 1.0659 time to fit residues: 219.0600 Evaluate side-chains 182 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 180 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 0.9990 chunk 83 optimal weight: 0.0770 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 86 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 99 optimal weight: 0.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 331 ASN C 88 ASN C 125 ASN C 295 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8833 Z= 0.201 Angle : 0.522 6.566 11993 Z= 0.281 Chirality : 0.041 0.183 1399 Planarity : 0.004 0.055 1503 Dihedral : 5.239 63.636 1272 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.82 % Allowed : 8.44 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.25), residues: 1100 helix: 1.67 (0.27), residues: 371 sheet: 0.51 (0.30), residues: 263 loop : -1.21 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 169 HIS 0.005 0.001 HIS C 62 PHE 0.013 0.001 PHE B 189 TYR 0.018 0.001 TYR E 178 ARG 0.004 0.000 ARG C 197 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 190 time to evaluate : 0.876 Fit side-chains REVERT: A 121 MET cc_start: 0.7420 (OUTLIER) cc_final: 0.6359 (ppp) REVERT: A 151 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7024 (tmm) REVERT: A 192 SER cc_start: 0.7586 (OUTLIER) cc_final: 0.7299 (m) REVERT: B 275 GLU cc_start: 0.7113 (tt0) cc_final: 0.6811 (tt0) REVERT: C 197 ARG cc_start: 0.7062 (mtm-85) cc_final: 0.6743 (mtm-85) REVERT: C 258 ASP cc_start: 0.6964 (t70) cc_final: 0.6666 (t0) REVERT: C 314 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7280 (ttm170) REVERT: E 89 GLU cc_start: 0.7179 (mp0) cc_final: 0.6811 (mp0) REVERT: E 93 MET cc_start: 0.7997 (tpp) cc_final: 0.7761 (tpt) outliers start: 17 outliers final: 3 residues processed: 195 average time/residue: 0.9990 time to fit residues: 209.6425 Evaluate side-chains 194 residues out of total 969 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 187 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 151 MET Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain C residue 227 SER Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain E residue 222 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 56.4244 > 50: distance: 68 - 73: 16.811 distance: 73 - 74: 17.184 distance: 74 - 75: 31.825 distance: 74 - 77: 7.364 distance: 75 - 76: 7.076 distance: 75 - 81: 10.270 distance: 77 - 78: 16.576 distance: 78 - 79: 6.327 distance: 78 - 80: 21.461 distance: 81 - 82: 21.859 distance: 82 - 83: 17.070 distance: 82 - 85: 31.570 distance: 83 - 84: 9.645 distance: 83 - 93: 29.428 distance: 85 - 86: 19.676 distance: 86 - 87: 11.636 distance: 86 - 88: 8.029 distance: 87 - 89: 7.695 distance: 88 - 90: 8.706 distance: 89 - 91: 5.611 distance: 90 - 91: 6.620 distance: 91 - 92: 11.963 distance: 93 - 94: 15.463 distance: 94 - 95: 9.095 distance: 94 - 97: 24.977 distance: 95 - 96: 19.306 distance: 95 - 98: 8.979 distance: 98 - 99: 15.351 distance: 99 - 100: 15.159 distance: 99 - 102: 4.957 distance: 100 - 101: 15.855 distance: 102 - 103: 8.007 distance: 103 - 104: 12.472 distance: 103 - 105: 4.278 distance: 104 - 106: 4.839 distance: 105 - 107: 8.190 distance: 107 - 108: 7.004 distance: 109 - 110: 8.925 distance: 110 - 111: 16.600 distance: 110 - 113: 5.093 distance: 111 - 112: 15.124 distance: 111 - 117: 16.748 distance: 113 - 114: 4.790 distance: 114 - 115: 9.759 distance: 114 - 116: 10.580 distance: 117 - 118: 14.848 distance: 118 - 119: 24.303 distance: 118 - 121: 11.937 distance: 119 - 120: 16.008 distance: 119 - 125: 25.913 distance: 120 - 153: 23.281 distance: 121 - 122: 12.597 distance: 122 - 123: 5.996 distance: 125 - 126: 18.284 distance: 126 - 127: 43.018 distance: 126 - 129: 17.407 distance: 127 - 128: 37.960 distance: 127 - 134: 56.424 distance: 129 - 130: 10.713 distance: 130 - 131: 14.542 distance: 131 - 132: 15.194 distance: 131 - 133: 12.712 distance: 134 - 135: 37.232 distance: 135 - 136: 30.167 distance: 135 - 138: 14.422 distance: 136 - 137: 19.572 distance: 136 - 142: 20.336 distance: 138 - 139: 10.995 distance: 139 - 140: 14.869 distance: 139 - 141: 10.700 distance: 142 - 143: 9.545 distance: 143 - 144: 18.687 distance: 143 - 146: 4.838 distance: 144 - 145: 14.091 distance: 144 - 153: 13.426 distance: 146 - 147: 4.469 distance: 147 - 148: 4.632 distance: 147 - 149: 4.598 distance: 148 - 150: 3.538 distance: 149 - 151: 6.710 distance: 150 - 152: 8.398 distance: 151 - 152: 10.005 distance: 153 - 154: 10.648 distance: 154 - 155: 3.650 distance: 154 - 157: 7.950 distance: 155 - 156: 9.654 distance: 155 - 162: 7.127 distance: 157 - 158: 8.790 distance: 158 - 159: 3.778 distance: 160 - 161: 3.104